Journal article
A HUPO test sample study reveals common problems in mass spectrometry-based proteomics
Nature methods, Vol.6(6), pp.423-U40
06/01/2009
DOI: 10.1038/NMETH.1333
PMCID: PMC2785450
PMID: 19448641
Abstract
We performed a test sample study to try to identify errors leading to irreproducibility, including incompleteness of peptide sampling, in liquid chromatography-mass spectrometry-based proteomics. We distributed an equimolar test sample, comprising 20 highly purified recombinant human proteins, to 27 laboratories. Each protein contained one or more unique tryptic peptides of 1,250 Da to test for ion selection and sampling in the mass spectrometer. Of the 27 labs, members of only 7 labs initially reported all 20 proteins correctly, and members of only 1 lab reported all tryptic peptides of 1,250 Da. Centralized analysis of the raw data, however, revealed that all 20 proteins and most of the 1,250 Da peptides had been detected in all 27 labs. Our centralized analysis determined missed identifications (false negatives), environmental contamination, database matching and curation of protein identifications as sources of problems. Improved search engines and databases are needed for mass spectrometry-based proteomics.
Details
- Title: Subtitle
- A HUPO test sample study reveals common problems in mass spectrometry-based proteomics
- Creators
- Alexander W. Bell - McGill UniversityEric W. Deutsch - Institute for Systems BiologyCatherine E. Au - McGill UniversityRobert E. Kearney - McGill UniversityRon Beavis - University of British ColumbiaSalvatore Sechi - National Institute of Diabetes and Digestive and Kidney DiseasesTommy Nilsson - McGill University Health CentreJohn J. M. Bergeron - McGill UniversityHuman Proteome Organization (HUPO) Test Sample Working GroupMarshall Pope (Contributor) - Medicine Administration
- Resource Type
- Journal article
- Publication Details
- Nature methods, Vol.6(6), pp.423-U40
- DOI
- 10.1038/NMETH.1333
- PMID
- 19448641
- PMCID
- PMC2785450
- NLM abbreviation
- Nat Methods
- ISSN
- 1548-7091
- eISSN
- 1548-7105
- Publisher
- Springer Nature
- Number of pages
- 11
- Grant note
- 2006CB910801; 2006AA02A308 / Beijing Proteome Research Center RR020843 / University of California, Los Angeles Burnham Institute for Medical Research NIH; University of California System P41RR018627 / University of Michigan, NIH; University of Michigan System; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA N01-HV-28179 / National Heart, Lung and Blood Institute, National Institutes of Health (NIH); United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Heart Lung & Blood Institute (NHLBI) P01-008111 / University of California, Los Angeles (National Heart, Lung and Blood Institute); United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Heart Lung & Blood Institute (NHLBI) 04/RPI/B499 / Science Foundation, Ireland; Science Foundation Ireland LSHG-CT-2006036814 / EU; European Union (EU) Spanish Ministry of Education and Science; Spanish Government
- Language
- English
- Date published
- 06/01/2009
- Academic Unit
- Medicine Administration
- Record Identifier
- 9984627298302771
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